It's not nice trying to do it in the database, you'll need to back everything up, shut down JIRA, hack the cwd_group and cwd_membership tables, plus the counter table (I don't know if embedded crowd uses the JIRA counters or its own), and fully understand exactly how they work to get the SQL correct. If you're not using embedded crowd, that all changes of course.
Users being in 300 groups sounds rather broken too. I suspect that if you're really using them for permissions, you're going to create performance issues in your JIRA. Rather than try to replicate a broken set of groups, it might be a good time to evaluate why you've got so many and simplify.
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